Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 86 of 235
Found at i:29900261 original size:84 final size:85
Alignment explanation
Indices: 29899733--29900261 Score: 774
Period size: 84 Copynumber: 6.3 Consensus size: 85
29899723 ATCATTTTGG
* * * *
29899733 ACCCTACTGCTTAGGGGGTTAAGGTGCATCGTCTTCGATCTGCTCCGCTACTGCTTA-GG-GATA
1 ACCCTACTGCTTAGGGGATTAAGGCG-A-GGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATA
29899796 AGATCTGCAAATTTAACCTGTT
64 AGATCTGCAAATTTAACCTGTT
29899818 ACCCTACTGCTTAGGGGATTAAGGC-AGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
1 ACCCTACTGCTTAGGGGATTAAGGCGAGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
*
29899882 ATCTGTAAATTTAACCTGTT
66 ATCTGCAAATTTAACCTGTT
29899902 ACCCTACTGCTTAGGGGATTAAGGC-AGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
1 ACCCTACTGCTTAGGGGATTAAGGCGAGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
*
29899966 ATCTGTAAATTTAACCTGTT
66 ATCTGCAAATTTAACCTGTT
* * * * **
29899986 ACCCTACTGCTTAGGGGATTAAGGTGAGTCGTCGTCGATCTGCTCCGCTACTGTTTAGACAGATA
1 ACCCTACTGCTTAGGGGATTAAGGCGAG--GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATA
* *
29900051 AGATCTGC-----GAACCTATT
64 AGATCTGCAAATTTAACCTGTT
29900068 ACCCTACTGCTTAGGGGATTAAGGCGA-GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
1 ACCCTACTGCTTAGGGGATTAAGGCGAGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
29900132 ATCTGCAAATTTAACCTGTT
66 ATCTGCAAATTTAACCTGTT
* * * *
29900152 ACCCTACTACTTAGGGGATTAAGGCGA-GACTTTGATCTACTCCACTACTGCTTAGGGAGATAAG
1 ACCCTACTGCTTAGGGGATTAAGGCGAGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
29900216 ATCTGCAAATTTAACCTGTT
66 ATCTGCAAATTTAACCTGTT
*
29900236 ACCCTACTACTTAGGGGATTAAGGCG
1 ACCCTACTGCTTAGGGGATTAAGGCG
29900262 TTGAATTTTG
Statistics
Matches: 408, Mismatches: 26, Indels: 21
0.90 0.06 0.05
Matches are distributed among these distances:
79 38 0.09
82 59 0.14
83 3 0.01
84 246 0.60
85 25 0.06
87 37 0.09
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (85 bp):
ACCCTACTGCTTAGGGGATTAAGGCGAGGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
ATCTGCAAATTTAACCTGTT
Found at i:29901250 original size:19 final size:18
Alignment explanation
Indices: 29901216--29901275 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
29901206 GGCCTCTCCA
*
29901216 TTTTTTTTTCTTTTTTCTT
1 TTTTTTTTTC-CTTTTCTT
29901235 TTTTCTTTTTCCTTTTCTT
1 TTTT-TTTTTCCTTTTCTT
*
29901254 TCCTTTTTTTCCTTTT-TT
1 T-TTTTTTTTCCTTTTCTT
29901272 TTTT
1 TTTT
29901276 GAAATAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.06
18 3 0.08
19 23 0.64
20 8 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTCCTTTTCTT
Found at i:29901269 original size:7 final size:7
Alignment explanation
Indices: 29901219--29901250 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
29901209 CTCTCCATTT
29901219 TTTTTTC
1 TTTTTTC
29901226 TTTTTTC
1 TTTTTTC
29901233 TTTTTTC
1 TTTTTTC
*
29901240 TTTTTCC
1 TTTTTTC
29901247 TTTT
1 TTTT
29901251 CTTTCCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:29906917 original size:22 final size:21
Alignment explanation
Indices: 29906891--29906932 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29906881 ATTAAATATC
29906891 CAAGATTACAAGATCATATCTT
1 CAAGATTAC-AGATCATATCTT
* *
29906913 CAAGATTGCATATCATATCT
1 CAAGATTACAGATCATATCT
29906933 AAGACTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
CAAGATTACAGATCATATCTT
Found at i:29906941 original size:19 final size:19
Alignment explanation
Indices: 29906903--29907000 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
29906893 AGATTACAAG
29906903 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
*
29906924 ATCATATCTAAGACTGCAT
1 ATCATATCTAAGATTGCAT
29906943 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
29906960 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
29906979 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
29906998 ATC
1 ATC
29907001 CTTAAAGATT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 17 0.23
19 47 0.64
20 1 0.01
21 8 0.11
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:29906967 original size:36 final size:37
Alignment explanation
Indices: 29906903--29907000 Score: 144
Period size: 36 Copynumber: 2.6 Consensus size: 37
29906893 AGATTACAAG
29906903 ATCATATCTTCAAGATTGCATATCATATCTAAGACTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGACTGCAT
*
29906943 ATCATATCTAAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGACTGCAT
29906979 ATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTG-ATATC
29907001 CTTAAAGATT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
36 35 0.64
38 11 0.20
39 1 0.02
40 8 0.15
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGACTGCAT
Found at i:29912841 original size:102 final size:102
Alignment explanation
Indices: 29912665--29912869 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 102
29912655 AACGAAGCAA
* *
29912665 GACACGGCCGTGTGCACCCACACGCCCAAGGAACACTGGCGTGGGGCGAATGTTAGACGCGCCTA
1 GACACGACCGTGTGCACCCACACGCCCAAGGAACACTGGCGTGGGACGAATGTTAGACGCGCCTA
29912730 AATTTAAAAATCGTGAAACACACGGGCACGGCCATGT
66 AATTTAAAAATCGTGAAACACACGGGCACGGCCATGT
* *
29912767 GACACGACCGTGTGTACCCACATGCCCAAGGAACACTGGCGTGGGACGAATGTTAGACGCGCCTA
1 GACACGACCGTGTGCACCCACACGCCCAAGGAACACTGGCGTGGGACGAATGTTAGACGCGCCTA
*
29912832 AATTTAAAAATCGTGAAACACACGGGCACGGCCGTGT
66 AATTTAAAAATCGTGAAACACACGGGCACGGCCATGT
29912869 G
1 G
29912870 CCCCAAAATC
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.16
Consensus pattern (102 bp):
GACACGACCGTGTGCACCCACACGCCCAAGGAACACTGGCGTGGGACGAATGTTAGACGCGCCTA
AATTTAAAAATCGTGAAACACACGGGCACGGCCATGT
Found at i:29913169 original size:48 final size:48
Alignment explanation
Indices: 29913113--29913334 Score: 363
Period size: 48 Copynumber: 4.6 Consensus size: 48
29913103 ATACTCATAG
29913113 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
* *
29913161 TAGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCACAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
* * *
29913209 TAGCCATTCGGCTTTACCACATATATATATCTCATACATATTTCATAT
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
*
29913257 TAGCCACTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
1 TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
* * *
29913305 TAGCCATTCAGCTTTACCACACATATATAT
1 TAGCCATTCGGCTTTACCACATATACATAT
29913335 ATTTATCTTG
Statistics
Matches: 161, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 161 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACAC
Found at i:29920430 original size:17 final size:17
Alignment explanation
Indices: 29920405--29920441 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
29920395 GTAAAATTTG
29920405 TTTAGCTATCAACAACC
1 TTTAGCTATCAACAACC
*
29920422 TTTATCTATCAACAACC
1 TTTAGCTATCAACAACC
29920439 TTT
1 TTT
29920442 CATTTTATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTAGCTATCAACAACC
Found at i:29924065 original size:44 final size:43
Alignment explanation
Indices: 29923997--29924083 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 43
29923987 TAAGAGAGAA
*
29923997 AGAGTGTAACATTCAGATTCTGGGCTTAGTTAGAACAGTGGTT
1 AGAGTGTAACATCCAGATTCTGGGCTTAGTTAGAACAGTGGTT
*
29924040 NAGAGTGTAACATCCAGATTTTGGGCTTAGTTAGAACAGTGGTT
1 -AGAGTGTAACATCCAGATTCTGGGCTTAGTTAGAACAGTGGTT
29924084 TCGGGACCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.32
Consensus pattern (43 bp):
AGAGTGTAACATCCAGATTCTGGGCTTAGTTAGAACAGTGGTT
Found at i:29925343 original size:49 final size:49
Alignment explanation
Indices: 29925266--29925361 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
29925256 TCTATTGTGA
* * *
29925266 GGTCACATGTGTTGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* *
29925315 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA
29925362 CTTTGGCTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:29930429 original size:49 final size:49
Alignment explanation
Indices: 29930357--29930534 Score: 171
Period size: 49 Copynumber: 3.6 Consensus size: 49
29930347 TGTGAGGTCA
* * * *
29930357 CATGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAA-TTGGTT
1 CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCCGATAACTTCGAT
* * *
29930405 GCATGTGTAGTATTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGAT
1 -CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCCGATAACTTCGAT
*** ** * *
29930455 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGAT-GGTTAGGT
1 CA--TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCCGATAACTTCGAT
29930505 CACGTGTGTAGTACTAAGTGCAGGCTACTA
1 CA--TGTGTAGTACTAAGTGCAGGCTACTA
29930535 TGCATACCAG
Statistics
Matches: 109, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
49 39 0.36
50 38 0.35
51 32 0.29
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCCGATAACTTCGAT
Found at i:29930536 original size:101 final size:100
Alignment explanation
Indices: 29930354--29930551 Score: 270
Period size: 101 Copynumber: 2.0 Consensus size: 100
29930344 TATTGTGAGG
* ** *
29930354 TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTTGCATGTGTAGTATT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCACATGTGTAGTACT
* *
29930419 AAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGCATACCAGATAACTTCGA
* * ** ** *
29930454 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATT-GGTCACATGTGTAGTAC
29930519 TAAGTGCAGGCTACTATGCATACCAGATAACTT
65 TAAGTGCAGGCTACTATGCATACCAGATAACTT
29930552 TGGCTACAAG
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 40 0.48
101 44 0.52
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGCATACCAGATAACTTCGA
Found at i:29935604 original size:208 final size:208
Alignment explanation
Indices: 29935246--29936001 Score: 1496
Period size: 208 Copynumber: 3.6 Consensus size: 208
29935236 AGGGTATTCG
29935246 GTTATTTAGAG-TAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTC
1 GTTATTTAG-GTTAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTC
29935310 AAACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCC
65 AAACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCC
29935375 GGTAAGTTAGGGCACAACACTTCGTACCTCCGAGAATGAGCATTTTCAAAACTTATATAGCGATT
130 GGTAAGTTAGGGCACAACACTTCGTACCTCCGAGAATGAGCATTTTCAAAACTTATATAGCGATT
29935440 TAAAAGAGTAGTCC
195 TAAAAGAGTAGTCC
29935454 GTTATTTAGGTTAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTCA
1 GTTATTTAGGTTAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTCA
29935519 AACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCCG
66 AACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCCG
29935584 GTAAGTTAGGGCACAACACTTCGTACCTCCGAGAATGAGCATTTTCAAAACTTATATAGCGATTT
131 GTAAGTTAGGGCACAACACTTCGTACCTCCGAGAATGAGCATTTTCAAAACTTATATAGCGATTT
29935649 AAAAGAGTAGTCC
196 AAAAGAGTAGTCC
29935662 GTTATTTAGGTTAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTCA
1 GTTATTTAGGTTAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTCA
29935727 AACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCCG
66 AACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCCG
29935792 GTAAGTTAGGGCACAACACTTCGTACCTCCGAGAATGAGCATTTTCAAAACTTATATAGCGATTT
131 GTAAGTTAGGGCACAACACTTCGTACCTCCGAGAATGAGCATTTTCAAAACTTATATAGCGATTT
29935857 AAAAGAGTAGTCC
196 AAAAGAGTAGTCC
29935870 GTTATTTAGGTTAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTCA
1 GTTATTTAGGTTAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTCA
29935935 AACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCCG
66 AACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCCG
29936000 GT
131 GT
29936002 NNNNNNNNNN
Statistics
Matches: 547, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
207 1 0.00
208 546 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (208 bp):
GTTATTTAGGTTAAACGAGAAAAATCGAAACCCAGTAAGTTGGGGTATGTTTTCCCGAATTCTCA
AACACCGAATATTGCCTTTGTTTTAAAACAAATTCATATTTCGAGGTGACAAAATGTCATACCCG
GTAAGTTAGGGCACAACACTTCGTACCTCCGAGAATGAGCATTTTCAAAACTTATATAGCGATTT
AAAAGAGTAGTCC
Found at i:29946245 original size:9 final size:9
Alignment explanation
Indices: 29946227--29946256 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29946217 TGCAATGCTG
29946227 ATGC-ATGA
1 ATGCGATGA
29946235 ATGCGATGA
1 ATGCGATGA
29946244 ATGCGATGA
1 ATGCGATGA
29946253 ATGC
1 ATGC
29946257 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.23
Consensus pattern (9 bp):
ATGCGATGA
Found at i:29950226 original size:23 final size:24
Alignment explanation
Indices: 29950163--29950226 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
29950153 ATGCATTGAG
29950163 ATATATACGTAATAATAGAAATAAA
1 ATATATACGTAAT-ATAGAAATAAA
* *
29950188 ATTTATACGTAGTATA-AAA-AAGA
1 ATATATACGTAATATAGAAATAA-A
*
29950211 ATATATACATAATATA
1 ATATATACGTAATATA
29950227 CATATATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 2 0.06
23 17 0.52
24 3 0.09
25 11 0.33
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (24 bp):
ATATATACGTAATATAGAAATAAA
Found at i:29958015 original size:37 final size:37
Alignment explanation
Indices: 29957962--29958101 Score: 244
Period size: 37 Copynumber: 3.8 Consensus size: 37
29957952 CGAATAGTCC
* *
29957962 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
29957999 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
**
29958036 CCACACGTAGTCATCAAGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
29958073 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
29958102 ATATATTTCC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
Found at i:29958354 original size:48 final size:48
Alignment explanation
Indices: 29958242--29959653 Score: 2313
Period size: 48 Copynumber: 29.9 Consensus size: 48
29958232 ATATACACAC
*
29958242 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTTTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGC----TTTACCACATATACAT
*
29958294 ACCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
29958342 ATCTCATTCATATTTCACACTAGCCATTTGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958388 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958436 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958484 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958532 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
29958580 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
29958628 ATCTCATACATATCTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958674 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958720 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958766 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958812 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958858 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958904 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958950 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29958996 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959042 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959088 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959134 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959180 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
29959226 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959274 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959322 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959370 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959418 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959466 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959514 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959562 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
29959610 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATAT
29959654 TCACTACAAG
Statistics
Matches: 1340, Mismatches: 16, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
46 638 0.48
48 672 0.50
52 30 0.02
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:29958761 original size:92 final size:93
Alignment explanation
Indices: 29958242--29959650 Score: 2272
Period size: 92 Copynumber: 14.9 Consensus size: 93
29958232 ATATACACAC
* * *
29958242 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTTTTTACCACATATACATACCTCATACATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGC----TTTACCAC--ACACATATCTCATACATAT
29958307 TTCACACTAGCCATTCGGCTTTACCACATATACAT
60 TTCACACTAGCCATTCGGCTTTACCACA-ATACAT
* * *
29958342 ATCTCATTCATATTTCACACTAGCCATTTGGCTTTACCACACACATATCTCATATATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
29958407 CTAGCCATTCGGCTTTACCACATATACAT
66 CTAGCCATTCGGCTTTACCACA-ATACAT
* * *
29958436 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACATATCTCATACATATTTCA
29958501 CACTAGCCATTCGGCTTTACCACATATACAT
64 CACTAGCCATTCGGCTTTACCACA-ATACAT
* *
29958532 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACATATCTCATACATATTTCA
29958597 CACTAGCCATTCGGCTTTACCACATATACAT
64 CACTAGCCATTCGGCTTTACCACA-ATACAT
*
29958628 ATCTCATACATATCTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
*
29958693 CTAGCCATTCGGCTTTACCAC-ACACAT
66 CTAGCCATTCGGCTTTACCACAATACAT
29958720 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
*
29958785 CTAGCCATTCGGCTTTACCAC-ACACAT
66 CTAGCCATTCGGCTTTACCACAATACAT
29958812 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
*
29958877 CTAGCCATTCGGCTTTACCAC-ACACAT
66 CTAGCCATTCGGCTTTACCACAATACAT
29958904 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
*
29958969 CTAGCCATTCGGCTTTACCAC-ACACAT
66 CTAGCCATTCGGCTTTACCACAATACAT
29958996 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
*
29959061 CTAGCCATTCGGCTTTACCAC-ACACAT
66 CTAGCCATTCGGCTTTACCACAATACAT
29959088 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
*
29959153 CTAGCCATTCGGCTTTACCAC-ACACAT
66 CTAGCCATTCGGCTTTACCACAATACAT
29959180 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
29959245 CTAGCCATTCGGCTTTACCACATATACAT
66 CTAGCCATTCGGCTTTACCACA-ATACAT
* * *
29959274 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACATATCTCATACATATTTCA
29959339 CACTAGCCATTCGGCTTTACCACATATACAT
64 CACTAGCCATTCGGCTTTACCACA-ATACAT
* * *
29959370 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACATATCTCATACATATTTCA
29959435 CACTAGCCATTCGGCTTTACCACATATACAT
64 CACTAGCCATTCGGCTTTACCACA-ATACAT
* * *
29959466 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACATATCTCATACATATTTCA
29959531 CACTAGCCATTCGGCTTTACCACATATACAT
64 CACTAGCCATTCGGCTTTACCACA-ATACAT
* * *
29959562 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC--ACACATATCTCATACATATTTCA
29959627 CACTAGCCATTCGGCTTTACCACA
64 CACTAGCCATTCGGCTTTACCACA
29959651 TATTCACTAC
Statistics
Matches: 1283, Mismatches: 20, Indels: 16
0.97 0.02 0.01
Matches are distributed among these distances:
92 550 0.43
94 177 0.14
96 527 0.41
100 29 0.02
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (93 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACACATATCTCATACATATTTCACA
CTAGCCATTCGGCTTTACCACAATACAT
Found at i:29962789 original size:30 final size:30
Alignment explanation
Indices: 29962755--29962814 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29962745 ATTTAATACG
29962755 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
29962785 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
29962815 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:29985287 original size:36 final size:36
Alignment explanation
Indices: 29985240--29985311 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
29985230 AAAAGCTGCA
* * * * *
29985240 ATAAATTTCACTTCAGAGAGTGCTGGATGAAGAGCG
1 ATAAAATTCACTTCAAAAAGTGCCGGATAAAGAGCG
*
29985276 ATAAAATTCACTTTAAAAAGTGCCGGATAAAGAGCG
1 ATAAAATTCACTTCAAAAAGTGCCGGATAAAGAGCG
29985312 GTGCGTGCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (36 bp):
ATAAAATTCACTTCAAAAAGTGCCGGATAAAGAGCG
Found at i:29993582 original size:12 final size:12
Alignment explanation
Indices: 29993565--29993589 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29993555 TTATTAAATG
29993565 AATTAAAAGCCA
1 AATTAAAAGCCA
29993577 AATTAAAAGCCA
1 AATTAAAAGCCA
29993589 A
1 A
29993590 TTTTTGTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AATTAAAAGCCA
Found at i:29996785 original size:40 final size:40
Alignment explanation
Indices: 29996740--29996976 Score: 429
Period size: 40 Copynumber: 5.9 Consensus size: 40
29996730 GCAAACACAT
*
29996740 TTGCCTTCGGGTCTTAGCCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
29996780 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
29996820 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
29996860 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
29996900 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
29996940 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCA
29996977 CATGCACACA
Statistics
Matches: 192, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 192 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:30000170 original size:30 final size:29
Alignment explanation
Indices: 30000105--30000171 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
30000095 TTTAAGTAAA
* **
30000105 ATGGACTAAATTGTGAAAATGTGAAATTG
1 ATGGACTAAACTGTGAAAAAATGAAATTG
*
30000134 AAGGACTAAACTGTGAAATAAATGAAATGTG
1 ATGGACTAAACTGTGAAA-AAATGAAAT-TG
30000165 -TGGACTA
1 ATGGACTA
30000172 GTATGAGTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 16 0.52
30 13 0.42
31 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.27
Consensus pattern (29 bp):
ATGGACTAAACTGTGAAAAAATGAAATTG
Found at i:30011479 original size:47 final size:47
Alignment explanation
Indices: 30011406--30011925 Score: 783
Period size: 47 Copynumber: 11.1 Consensus size: 47
30011396 GAAATGATAG
* *
30011406 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* *
30011453 TAAGGCCTAATAGCCGACGTGGTGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
30011500 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
30011547 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
30011594 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
30011641 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
30011688 TAAGGCCTAATAGCTGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
30011735 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATAG-GTAA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT-GTGTGA
* *
30011782 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* * *
30011829 TGAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* * * * * * * * * **
30011875 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
30011922 TAAG
1 TAAG
30011926 TCCCGAAGGG
Statistics
Matches: 443, Mismatches: 27, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
46 39 0.09
47 403 0.91
48 1 0.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
Found at i:30012100 original size:37 final size:37
Alignment explanation
Indices: 30012044--30012122 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
30012034 CCGAGCTCTA
* * *
30012044 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
30012081 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
30012118 AAGAC
1 AAGAC
30012123 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:30017426 original size:40 final size:39
Alignment explanation
Indices: 30017328--30017510 Score: 188
Period size: 40 Copynumber: 4.6 Consensus size: 39
30017318 TCCTCGTTCA
* * *
30017328 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* *
30017367 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* *
30017406 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* * * * * *
30017446 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCA-CAC
* *
30017487 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
30017511 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 39 0.32
40 76 0.63
41 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
Found at i:30029875 original size:12 final size:12
Alignment explanation
Indices: 30029858--30029882 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30029848 TTATTAAATG
30029858 AATTAAAAGCCA
1 AATTAAAAGCCA
30029870 AATTAAAAGCCA
1 AATTAAAAGCCA
30029882 A
1 A
30029883 TTTTTGCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AATTAAAAGCCA
Found at i:30037787 original size:6 final size:6
Alignment explanation
Indices: 30037776--30037810 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
30037766 CCTATCTTTT
30037776 TTATTC TTATTC TTATTC TTATTC TTATTC TTATT
1 TTATTC TTATTC TTATTC TTATTC TTATTC TTATT
30037811 TTCATTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATTC
Found at i:30042473 original size:42 final size:42
Alignment explanation
Indices: 30042428--30042583 Score: 170
Period size: 42 Copynumber: 3.7 Consensus size: 42
30042418 CAAGACTATG
* *
30042428 TGTAAGACCATATCTGGGATATGGCATTAATATGAGATTTTG
1 TGTAAGACCATATCTGGGATATGGCATTGATATGAGATTTTA
* *
30042470 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATTGATATGAGATTTTA
* * * * * **
30042512 TGTAAGACCGTAGCTAGGCTATTGGAATTGATACT-AGATCCTA
1 TGTAAGACCATATCTGGGATA-TGGCATTGATA-TGAGATTTTA
* *
30042555 TGTAAGATCATATCTGGGTTATGGCATTG
1 TGTAAGACCATATCTGGGATATGGCATTG
30042584 GTGTAGTACT
Statistics
Matches: 93, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
42 62 0.67
43 30 0.32
44 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATTGATATGAGATTTTA
Found at i:30047762 original size:3 final size:3
Alignment explanation
Indices: 30047754--30047787 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
30047744 TAAATAATGC
30047754 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
30047788 GTCATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:30052838 original size:55 final size:55
Alignment explanation
Indices: 30052711--30053117 Score: 573
Period size: 55 Copynumber: 7.5 Consensus size: 55
30052701 AATTTACTAT
* *
30052711 TGCCATGTCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-G-AACTCACCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAA
* *
30052764 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
30052819 TGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
* * * *
30052874 TGCCATGTCTTGACATGGTCTTACATGGTATCC-TCGTCTTAT-G-AACTCACCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAA
30052927 TGCCAT-TCCTT-AGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGT-CTTGA-CATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
30052982 TGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
*** *
30053037 TGCCATGTCTTGACATGGTCTTACATGATTTCC-TTGCCTTATAG-AACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATG-GGACCTTTGCCTTATAGTAACTCATCAA
* *
30053091 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGTCTTGACATGGTCTTACATG
30053118 ATATCCTTAT
Statistics
Matches: 322, Mismatches: 20, Indels: 23
0.88 0.05 0.06
Matches are distributed among these distances:
52 6 0.02
53 77 0.24
54 37 0.11
55 196 0.61
56 6 0.02
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (55 bp):
TGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
Found at i:30052921 original size:108 final size:108
Alignment explanation
Indices: 30052711--30053117 Score: 565
Period size: 108 Copynumber: 3.7 Consensus size: 108
30052701 AATTTACTAT
* *
30052711 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGGGA-CCTTGCCTTATAGAACTCATCAATGCCATGCCTT
*
30052775 GGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
65 GACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
*
30052819 TGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCT
1 TGCCATGTCTTGACATGGTCTTACATGGGACC-TTGCCTTATAG-AACTCATCAATGCCATGCCT
* * * *
30052884 TGACATGGTCTTACATGGTATCC-TCGTCTTAT-G-AACTCACCAA
64 TGACATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATCAA
*
30052927 TGCCAT-TCCTT-AGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGT
1 TGCCATGT-CTTGA-CATGGTCTTACATGGGACC-TTGCCTTATAG-AACTCATCAATGCCATGC
30052990 CTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
62 CTTGACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
*** *
30053037 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATG-GGACCTTGCCTTATAGAACTCATCAATGCCATGCCTT
*
30053102 GGCATGGTCTTACATG
65 GACATGGTCTTACATG
30053118 ATATCCTTAT
Statistics
Matches: 269, Mismatches: 18, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
107 6 0.02
108 134 0.50
109 37 0.14
110 86 0.32
111 6 0.02
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (108 bp):
TGCCATGTCTTGACATGGTCTTACATGGGACCTTGCCTTATAGAACTCATCAATGCCATGCCTTG
ACATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
Found at i:30052981 original size:163 final size:163
Alignment explanation
Indices: 30052711--30053117 Score: 733
Period size: 163 Copynumber: 2.5 Consensus size: 163
30052701 AATTTACTAT
30052711 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
30052776 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTT
66 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTT
30052841 ACATGGGACCTTTGCCTTATAGTAACTCATCAA
131 ACATGGGACCTTTGCCTTATAGTAACTCATCAA
* * * *
30052874 TGCCATGTCTTGACATGGTCTTACATGGTATCCTCGTCTTATGAACTCACCAATGCCATTCCTTA
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
30052939 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTT
66 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTT
30053004 ACATGGGACCTTTGCCTTATAGTAACTCATCAA
131 ACATGGGACCTTTGCCTTATAGTAACTCATCAA
* * * *
30053037 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
30053102 GGCATGGTCTTACATG
65 GGCATGGTCTTACATG
30053118 ATATCCTTAT
Statistics
Matches: 231, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
163 197 0.85
164 34 0.15
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (163 bp):
TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTT
ACATGGGACCTTTGCCTTATAGTAACTCATCAA
Found at i:30053366 original size:44 final size:44
Alignment explanation
Indices: 30053318--30053401 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
30053308 TCCTTAACAG
* *
30053318 TCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTTCCA
1 TCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTTCCA
* *
30053362 TCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
30053402 GAGATATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (44 bp):
TCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTTCCA
Found at i:30057256 original size:27 final size:27
Alignment explanation
Indices: 30057226--30057403 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
30057216 ATATTGAGCC
* *
30057226 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
30057253 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
30057280 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
30057308 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
30057335 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
30057362 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
30057389 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30057404 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:30057338 original size:55 final size:54
Alignment explanation
Indices: 30057226--30057403 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
30057216 ATATTGAGCC
* * * * *
30057226 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
30057280 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
30057335 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
30057389 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30057404 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:30065265 original size:27 final size:27
Alignment explanation
Indices: 30065235--30065412 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
30065225 ATATTGAGTC
* * * *
30065235 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
30065262 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
30065289 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
30065317 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
30065344 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
30065371 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
30065398 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30065413 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:30065374 original size:82 final size:81
Alignment explanation
Indices: 30065256--30065411 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
30065246 TGCTATATAA
* *
30065256 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
30065321 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
30065338 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
30065402 CACTTAGTGC
65 CACTTAGTGC
30065412 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:30073112 original size:44 final size:46
Alignment explanation
Indices: 30073012--30073173 Score: 181
Period size: 44 Copynumber: 3.6 Consensus size: 46
30073002 AGATGCCGAC
*
30073012 GCCATGTCCTAGACATGGTCTTACACTGGCTAGCACATCAAAGTCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTA-CACATCAAAGTCGAT
* ***
30073060 GCCATGTCCCAGACAGGTCTTACACTGGCT-C-TATCTGTGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTACACATCAAAGTCGAT
* * *
30073104 GCCATGTCCCAGACAGGTCTTACACTGAC-ACACAAC-AAG-CTGAC
1 GCCATGTCCCAGACAGGTCTTACACTGGCTACACATCAAAGTC-GAT
*
30073148 GCCATGTCCCAAACAGGTCTTACACT
1 GCCATGTCCCAGACAGGTCTTACACT
30073174 AGCTTTTATA
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.01
44 66 0.67
45 3 0.03
47 15 0.15
48 14 0.14
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (46 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTACACATCAAAGTCGAT
Found at i:30073221 original size:48 final size:46
Alignment explanation
Indices: 30073150--30073267 Score: 121
Period size: 46 Copynumber: 2.5 Consensus size: 46
30073140 AAGCTGACGC
* * * * *
30073150 CATGTCCCAAACAGGTCTTACACTAGCTTTTATATCTCGAA-GCAGATG
1 CATGTCCCAGACATGCCTTACACTAGC-TCT-CATCTC-AATGCAGATG
* * *
30073198 CATGTCCCAGATATGCCTTACACTAGCTCTCGTCTCAATGCCGATG
1 CATGTCCCAGACATGCCTTACACTAGCTCTCATCTCAATGCAGATG
*
30073244 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGCCTTACACT
30073268 GACTCTCGTA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 2 0.03
46 32 0.54
47 2 0.03
48 23 0.39
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGCCTTACACTAGCTCTCATCTCAATGCAGATG
Found at i:30077520 original size:40 final size:41
Alignment explanation
Indices: 30077421--30077526 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 41
30077411 TTAGCCGGAC
* *
30077421 ATAA-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGAAT
1 ATAAGCAACTCGCACAAATGCCTTCGGGACATAGCCCGAAT
* * *
30077461 ATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGAAT
1 ATAAGCAACTCGCACAAATGCCTTCGGGACATAGCCCGAAT
*
30077501 AT-AGCAACTCGCACGAATGCCTTCGG
1 ATAAGCAACTCGCACAAATGCCTTCGG
30077527 ATCTTAGTCC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.04
40 53 0.95
41 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (41 bp):
ATAAGCAACTCGCACAAATGCCTTCGGGACATAGCCCGAAT
Found at i:30084888 original size:40 final size:40
Alignment explanation
Indices: 30084818--30085035 Score: 359
Period size: 40 Copynumber: 5.5 Consensus size: 40
30084808 AACCCAAGTA
* *
30084818 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
30084857 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
30084897 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
30084937 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
30084977 TCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
30085017 CCTTTGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
30085036 TTATCATCCG
Statistics
Matches: 168, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 14 0.08
40 154 0.92
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:30090511 original size:48 final size:48
Alignment explanation
Indices: 30090393--30090662 Score: 353
Period size: 48 Copynumber: 5.6 Consensus size: 48
30090383 ATGAGATCCC
** * * *
30090393 GTGTAAGACCATGTCTGGGACATGGCATCGGCATCCAAGATGGGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGATATGTGTGCCA
* *
30090442 GTGTAAGACCATGTCTGGGACATGACATCGGCGTTGATATGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGTGCCA
*
30090490 GTGTAAGACCATGTCTAGGACATGGCATCGGCATTGATATGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGTGCCA
* * * * *
30090538 GTGTAATACCATGTCTAGGACATGGCATCGGTATTGATATATGTGTCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGTGCCA
* * *
30090586 GTATAAGACCATGTCTGGGACATGGCATCGGTGA-TGATATGTGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGATATGTGTGCCA
* *
30090634 GTATAAGACCATGTCTGGGAGATGGCATC
1 GTGTAAGACCATGTCTGGGACATGGCATC
30090663 ATCACCGATA
Statistics
Matches: 198, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
48 165 0.83
49 33 0.17
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGTGCCA
Found at i:30090686 original size:48 final size:48
Alignment explanation
Indices: 30090396--30090701 Score: 162
Period size: 48 Copynumber: 6.4 Consensus size: 48
30090386 AGATCCCGTG
* * * * *
30090396 TAAGACCATGTCTGGGACATGGCATCGGCATC-CAAGATG-GGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATC-G-ATCACGATATGAGTA-CTAGTA
* * ** * * * *
30090445 TAAGACCATGTCTGGGACATGACATCG-GCGTTGATATGTGTGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGATC-ACGATATGAGTACTAGTA
* * * * * * *
30090493 TAAGACCATGTCTAGGACATGGCATCG-GCATTGATATGTGTGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGATCA-CGATATGAGTACTAGTA
* * * * *
30090541 TAATACCATGTCTAGGACATGGCATCGGT-ATTGATAT-ATGT-GTCAGTA
1 TAAGACCATGTCTGGGACATGGCATCGATCA-CGATATGA-GTACT-AGTA
* * * * *
30090589 TAAGACCATGTCTGGGACATGGCATCGGTGATGATATGTGTGCTAGTA
1 TAAGACCATGTCTGGGACATGGCATCGATCACGATATGAGTACTAGTA
* *
30090637 TAAGACCATGTCTGGGAGATGGCATC-ATCACCGATATGAG-ACTTCGTA
1 TAAGACCATGTCTGGGACATGGCATCGATCA-CGATATGAGTAC-TAGTA
*
30090685 TAAGACCATATCTGGGA
1 TAAGACCATGTCTGGGA
30090702 TACGGTGTCG
Statistics
Matches: 217, Mismatches: 28, Indels: 25
0.80 0.10 0.09
Matches are distributed among these distances:
46 1 0.00
47 3 0.01
48 185 0.85
49 28 0.13
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATCGATCACGATATGAGTACTAGTA
Found at i:30095243 original size:49 final size:50
Alignment explanation
Indices: 30095163--30095395 Score: 299
Period size: 49 Copynumber: 4.7 Consensus size: 50
30095153 ATCTATTGTG
*
30095163 AGGTCACATGTGTAGTACTAAGTGCACGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
30095213 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * **
30095263 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
** * *
30095313 AGGTCATGTGTGTAGTATTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
30095363 -GGTCACATGTGTAGTACTAAGTGCAGGATACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
30095396 TGCGTACTAG
Statistics
Matches: 155, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
49 71 0.46
50 46 0.30
51 38 0.25
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:30098517 original size:15 final size:15
Alignment explanation
Indices: 30098499--30098531 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30098489 TGGATTCTCG
30098499 TATCATGGATTTCTT
1 TATCATGGATTTCTT
*
30098514 TATCTTGGATTTCTT
1 TATCATGGATTTCTT
30098529 TAT
1 TAT
30098532 TCTCGACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (15 bp):
TATCATGGATTTCTT
Found at i:30101357 original size:51 final size:48
Alignment explanation
Indices: 30101280--30101472 Score: 181
Period size: 48 Copynumber: 3.9 Consensus size: 48
30101270 CTATTGTGAG
* *
30101280 GTCACGTGTGTAGTACTAACTACAGGCTACTATGCGTACCCGATAACTT
1 GTCACGTGTGTAGTACTAACTGCAGGCTACTATGCGTACCAGATAA-TT
* * * * **
30101329 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 -G-TCACGTGTGTAGTACTAACTGCAGGCTACTATGCGTACCAGATAATT
* * * * *
30101379 GCCATGTGTGTAGTACTAACTGCAGGCTACTACT-TGTACCGGCTAATT
1 GTCACGTGTGTAGTACTAACTGCAGGCTACTA-TGCGTACCAGATAATT
* * * *
30101427 GGTCTCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAGATA
1 -GTCACGTGTGTAGTACTAACTGCAGGCTACTATGCGTACCAGATA
30101473 GCCTTGTCTA
Statistics
Matches: 113, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
48 38 0.34
49 35 0.31
50 3 0.03
51 37 0.33
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (48 bp):
GTCACGTGTGTAGTACTAACTGCAGGCTACTATGCGTACCAGATAATT
Found at i:30105993 original size:48 final size:48
Alignment explanation
Indices: 30105882--30106088 Score: 220
Period size: 48 Copynumber: 4.3 Consensus size: 48
30105872 ATGAGATCTC
* * * * * * * * *
30105882 GTGTAAGAGCATGTCTAGCACATGGCATTGGCATCAGAGATGGGAGCCA
1 GTGTAAGACCATGTTTGGGACATGGCATCGGCAT-TGATATGTGTGCCA
*
30105931 GTGTAAGACCATGTTTGGGACATGGCATTC-GTATTGATATGTGTGCCA
1 GTGTAAGACCATGTTTGGGACATGGCA-TCGGCATTGATATGTGTGCCA
* *
30105979 ATGTAAGACCATGTTTGGGACATGGCATCGGCGTTGATATGTGTGCCA
1 GTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGTGTGCCA
* * * *
30106027 GTGTAAGACCATGTCTGGGACATGACATCGACGA-TGATATGTGTGCTA
1 GTGTAAGACCATGTTTGGGACATGGCATCGGC-ATTGATATGTGTGCCA
*
30106075 GTGTAACACCATGT
1 GTGTAAGACCATGT
30106089 CCAAGACATG
Statistics
Matches: 135, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
47 2 0.01
48 106 0.79
49 26 0.19
50 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (48 bp):
GTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGTGTGCCA
Found at i:30106089 original size:48 final size:48
Alignment explanation
Indices: 30105927--30106103 Score: 223
Period size: 48 Copynumber: 3.7 Consensus size: 48
30105917 AGAGATGGGA
*
30105927 GCCAGTGTAAGACCATGTTTGGGACATGGCATTCGTA--TTGATATGTGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCA-TCG-ACGTTGATATGTGT
* * *
30105975 GCCAATGTAAGACCATGTTTGGGACATGGCATCGGCGTTGATATGTGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACGTTGATATGTGT
* *
30106023 GCCAGTGTAAGACCATGTCTGGGACATGACATCGACGATGATATGTGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACGTTGATATGTGT
* * ***
30106071 GCTAGTGTAACACCATGTCCAAGACATGGCATC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC
30106104 AGCACCGATA
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
47 3 0.03
48 111 0.97
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGACGTTGATATGTGT
Found at i:30114356 original size:49 final size:47
Alignment explanation
Indices: 30114218--30114397 Score: 315
Period size: 47 Copynumber: 3.8 Consensus size: 47
30114208 GCTCAGCTTT
*
30114218 GGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATC
1 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
30114265 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
1 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
30114312 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATC
1 GGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATC
* *
30114361 GGCCATTAGGCCTTATCACATATATATACATTCACAT
1 GGCCATTAGGCCTTATCACATATATACACTTTCACAT
30114398 CACAATTATC
Statistics
Matches: 128, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
47 81 0.63
49 47 0.37
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
Found at i:30114380 original size:96 final size:94
Alignment explanation
Indices: 30114218--30114397 Score: 315
Period size: 96 Copynumber: 1.9 Consensus size: 94
30114208 GCTCAGCTTT
*
30114218 GGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
1 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
*
30114283 CATATATACACTTTCACATTCATCACATC
66 CATATATACACATTCACATTCATCACATC
30114312 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 GGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
*
30114377 CACATATATATACATTCACAT
64 CACATATATACACATTCACAT
30114398 CACAATTATC
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
94 18 0.22
96 63 0.78
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (94 bp):
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
CATATATACACATTCACATTCATCACATC
Found at i:30117767 original size:40 final size:40
Alignment explanation
Indices: 30117722--30118162 Score: 663
Period size: 40 Copynumber: 11.1 Consensus size: 40
30117712 CGAATACACG
* * * *
30117722 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * * * *
30117762 ACACCAGCACGAATGCTCTTCGAGG-TTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCG-GGACTTAGCCCGGATACA
* * *
30117802 TTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
30117842 TCACTAGCATGAATGCTCTTCGGGACTTAGTCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
30117882 TCACTAGCATGAATGCTCTTCGGGACTTAGTCCAGG-TACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAG-CCCGGATACA
*
30117922 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
30117962 TCACTAGCATGAATGCTCTTCGGGACTTAGCTCGGGTACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
30118002 TCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
30118042 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
30118082 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGGTACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
30118122 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
30118161 TC
1 TC
30118163 GTTGAGACCT
Statistics
Matches: 367, Mismatches: 30, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
39 9 0.02
40 353 0.96
41 5 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:30120453 original size:47 final size:47
Alignment explanation
Indices: 30120375--30120684 Score: 487
Period size: 47 Copynumber: 6.6 Consensus size: 47
30120365 CCCTTCGGGA
* * * * * *
30120375 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30120421 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30120469 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
30120516 CTCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30120563 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
30120612 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
30120659 CTTATCACATATATACACTTTCACAT
1 CTTATCACATATATACACTTTCACAT
30120685 CACAATTATC
Statistics
Matches: 246, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
46 2 0.01
47 195 0.79
48 2 0.01
49 47 0.19
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:30120634 original size:143 final size:141
Alignment explanation
Indices: 30120378--30120685 Score: 483
Period size: 143 Copynumber: 2.2 Consensus size: 141
30120368 TTCGGGACTT
* * * * *
30120378 ATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCTCTGTCACATATATACACTTT
1 ATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCTCTATCACATATATACACTTT
*
30120443 CACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
66 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
30120508 CATTAGGCCTC
131 CATTAGGCCTC
* *
30120519 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC-CTTATCACATATATATACAC
1 ATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCTC-TATCAC--ATATATACAC
*
30120583 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATT
63 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
* *
30120648 GGCCATTCGGCCTT
128 GGCCATTAGGCCTC
30120662 ATCACATATATACACTTTCACATC
1 ATCACATATATACACTTTCACATC
30120686 ACAATTATCC
Statistics
Matches: 152, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
140 1 0.01
141 43 0.28
143 108 0.71
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (141 bp):
ATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCTCTATCACATATATACACTTT
CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC
CATTAGGCCTC
Found at i:30124196 original size:12 final size:12
Alignment explanation
Indices: 30124179--30124204 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30124169 CCACACACAC
30124179 CCGTGTGCTAGG
1 CCGTGTGCTAGG
30124191 CCGTGTGCTAGG
1 CCGTGTGCTAGG
30124203 CC
1 CC
30124205 ATGCCAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.38, T:0.23
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:30128167 original size:23 final size:24
Alignment explanation
Indices: 30128135--30128179 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
30128125 TAGATAAATT
* *
30128135 TATTGTTTTATTT-ATTGATGATA
1 TATTGATTTATTTGAATGATGATA
30128158 TATTGATTTATTTGAATGATGA
1 TATTGATTTATTTGAATGATGA
30128180 GTCCGAGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (24 bp):
TATTGATTTATTTGAATGATGATA
Found at i:30135103 original size:27 final size:27
Alignment explanation
Indices: 30135067--30135153 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
30135057 CTGACAGGGT
*
30135067 CACCACAACAGAAAATTGTGGCAGAGC
1 CACCAGAACAGAAAATTGTGGCAGAGC
* *
30135094 CACCAGAACAG-ATATATGTGCCAGAGC
1 CACCAGAACAGAAAAT-TGTGGCAGAGC
* * *
30135121 CACCAGATCAGATAATTGTGGCATAGC
1 CACCAGAACAGAAAATTGTGGCAGAGC
30135148 CACCAG
1 CACCAG
30135154 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 3 0.06
27 45 0.90
28 2 0.04
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (27 bp):
CACCAGAACAGAAAATTGTGGCAGAGC
Found at i:30135140 original size:54 final size:53
Alignment explanation
Indices: 30135043--30135153 Score: 141
Period size: 54 Copynumber: 2.1 Consensus size: 53
30135033 TGCATGGCTG
* *
30135043 CCAGAACAGATAATCTGACAGGGTCACCACAACAGAAAATTGTGGCAGAGCCA
1 CCAGAACAGATAATCTGACAGAGCCACCACAACAGAAAATTGTGGCAGAGCCA
* * * * * *
30135096 CCAGAACAGATATATGTGCCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATCTGACAGAGCCACCACAACAGAAAATTGTGGCAGAGCCA
30135150 CCAG
1 CCAG
30135154 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 12 0.24
54 37 0.76
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (53 bp):
CCAGAACAGATAATCTGACAGAGCCACCACAACAGAAAATTGTGGCAGAGCCA
Found at i:30140903 original size:46 final size:46
Alignment explanation
Indices: 30140851--30140978 Score: 184
Period size: 46 Copynumber: 2.8 Consensus size: 46
30140841 GGTTGAGCAT
* *
30140851 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * * *
30140897 CTGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGTATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* *
30140943 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
30140979 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:30145630 original size:27 final size:27
Alignment explanation
Indices: 30145576--30145686 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
30145566 AGCATGGCTG
* * *
30145576 CCAGAACAGATAA-TGTGACAGGGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
30145602 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
30145629 CCAAAACAGAT-ATATGTGGCAGAACCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
30145656 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
30145683 CCAG
1 CCAG
30145687 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 15 0.21
27 56 0.77
28 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:30146909 original size:16 final size:16
Alignment explanation
Indices: 30146884--30146916 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
30146874 CCAAAAGAAA
30146884 AAGAAAAGATGAGCAG
1 AAGAAAAGATGAGCAG
*
30146900 AAGAAGAGATGAGCAG
1 AAGAAAAGATGAGCAG
30146916 A
1 A
30146917 GAATTTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.33, T:0.06
Consensus pattern (16 bp):
AAGAAAAGATGAGCAG
Found at i:30168866 original size:40 final size:40
Alignment explanation
Indices: 30168811--30168992 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
30168801 TATTCGAATG
*
30168811 ATATCCGGTCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
30168851 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
30168891 ATATCCGAGCCAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
30168931 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
30168971 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
30168993 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 14 0.11
40 114 0.88
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:30170138 original size:14 final size:14
Alignment explanation
Indices: 30170119--30170160 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
30170109 CCTGACCAAA
30170119 AATTCTAGAAAAAC
1 AATTCTAGAAAAAC
30170133 AATTCTAGAAAAAC
1 AATTCTAGAAAAAC
30170147 AATTCTAGAAAAAC
1 AATTCTAGAAAAAC
30170161 TGTACTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AATTCTAGAAAAAC
Found at i:30177104 original size:46 final size:46
Alignment explanation
Indices: 30177054--30177229 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
30177044 TGGTTGAGCA
*
30177054 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
30177100 TCCGAACTCGTTGAGTTGAGTCCAAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
30177145 CATCCGAACTCGTTGAGTTGAGTCCGACTTTACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
30177193 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
30177230 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 59 0.56
47 26 0.25
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:30177188 original size:93 final size:93
Alignment explanation
Indices: 30177051--30177222 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
30177041 GGATGGTTGA
* * *
30177051 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGACTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
30177116 TGAGTCCAAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
* *
30177144 GCATCCGAACTCGTTGAGTTGAGTCCGACTTTACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGACTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
*
30177209 TGAGTCCGAGTTCG
66 TGAGTCCAAGTTCG
30177223 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGACTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:30179733 original size:40 final size:40
Alignment explanation
Indices: 30179678--30179859 Score: 269
Period size: 40 Copynumber: 4.6 Consensus size: 40
30179668 TATTCGAATG
*
30179678 ATATCCGGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
30179718 ATATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
30179758 ATATCCGGGCCAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
30179798 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGCTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
30179838 ATATCCGGG-TAAATCCTGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
30179860 TACTTGGGTT
Statistics
Matches: 129, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 10 0.08
40 117 0.91
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:30203916 original size:40 final size:40
Alignment explanation
Indices: 30203861--30203938 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
30203851 NNNNNNNNNN
30203861 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
30203901 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
30203939 GTTACATCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:30223779 original size:40 final size:40
Alignment explanation
Indices: 30223748--30223959 Score: 261
Period size: 40 Copynumber: 5.3 Consensus size: 40
30223738 GGACTAAGAT
30223748 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
30223788 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
* *
30223828 CCGAAGGCCTTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
* * * *
30223868 CCGAAGGCATTCGTGCGAGTTATTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCC
* * * * * *
30223908 CCGAAGGCA-TTGTGTGAGTTACTAAA-ACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
30223947 CCGAAGGCATTTG
1 CCGAAGGCATTTG
30223960 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 12, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
39 32 0.21
40 121 0.78
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
Found at i:30223977 original size:79 final size:80
Alignment explanation
Indices: 30223696--30223992 Score: 214
Period size: 80 Copynumber: 3.7 Consensus size: 80
30223686 TGAATGCTGT
* ** * * * ** **
30223696 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCCAT
*
30223759 TGTGCGAGATAC-AAATT
64 TGTGCGAGATACTAAA-A
* * * ** * *
30223776 CCGGGTTAAGCCCCGAAGGCATTTGTGCGAGAT-AC-AAATTCCGGGTTAAGCCCCGAAGGCCTT
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAA-TCCGGGTTAAGTCCCGAAGGCCAT
*
30223839 TGTGCGAGATACTAAAT
64 TGTGCGAGATACTAAAA
* ** * *
30223856 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG-CATTG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCCATTG
* *
30223920 TGTGAGTTACTAAAA
66 TGCGAGATACTAAAA
* * * *
30223935 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
30223993 TACGTGATTT
Statistics
Matches: 183, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
78 16 0.09
79 51 0.28
80 102 0.56
81 14 0.08
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCCATTG
TGCGAGATACTAAAA
Found at i:30231519 original size:27 final size:27
Alignment explanation
Indices: 30231464--30231523 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
30231454 GACATTTCAA
* * *
30231464 TCATTTTACCACATAAGGGCTATAAAG
1 TCATTTTACCACAAAAGGGCAAAAAAG
30231491 TCATTTTACCACAAAAGGG-AAAAATAG
1 TCATTTTACCACAAAAGGGCAAAAA-AG
30231518 TCATTT
1 TCATTT
30231524 CATCAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (27 bp):
TCATTTTACCACAAAAGGGCAAAAAAG
Found at i:30232961 original size:27 final size:27
Alignment explanation
Indices: 30232931--30232992 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
30232921 GGGACATTTC
* *
30232931 AGTCATTTTACCATAGAACGGTAAAAT
1 AGTCATTTTACCACAAAACGGTAAAAT
*
30232958 AGTCATTTTATCACAAAACGGTAAAAT
1 AGTCATTTTACCACAAAACGGTAAAAT
30232985 AGTCATTT
1 AGTCATTT
30232993 CATCAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (27 bp):
AGTCATTTTACCACAAAACGGTAAAAT
Found at i:30236470 original size:48 final size:48
Alignment explanation
Indices: 30236399--30236542 Score: 216
Period size: 48 Copynumber: 3.0 Consensus size: 48
30236389 CGAAAGTCTT
* * * *
30236399 GCACCCTAGGTGCCAATATCATGGCTTGAAGCCAAATCAATGAAGCTC
1 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
30236447 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
1 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
* * * *
30236495 ACACCCGAAGTGCTAATATCATGGCTCGAAACCAGATCAATAAAGCTC
1 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
30236543 CTAAGGACAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (48 bp):
GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
Found at i:30236473 original size:27 final size:27
Alignment explanation
Indices: 30236443--30236522 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
30236433 AATCAATGAA
30236443 GCTCGCACCCGAAGTGCTAATATCATG
1 GCTCGCACCCGAAGTGCTAATATCATG
* * *
30236470 GCTCGAAGCC-AAAT-C-AATGA--A--
1 GCTCGCACCCGAAGTGCTAAT-ATCATG
*
30236491 GCTCACACCCGAAGTGCTAATATCATG
1 GCTCGCACCCGAAGTGCTAATATCATG
30236518 GCTCG
1 GCTCG
30236523 AAACCAGATC
Statistics
Matches: 37, Mismatches: 8, Indels: 16
0.61 0.13 0.26
Matches are distributed among these distances:
21 7 0.19
22 3 0.08
23 3 0.08
24 6 0.16
25 3 0.08
26 3 0.08
27 12 0.32
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (27 bp):
GCTCGCACCCGAAGTGCTAATATCATG
Found at i:30240023 original size:14 final size:14
Alignment explanation
Indices: 30240004--30240045 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
30239994 ACGAGGCTCA
30240004 TTTGCTTCCTTTGC
1 TTTGCTTCCTTTGC
*
30240018 TTTGCTTCCTTCGC
1 TTTGCTTCCTTTGC
30240032 TTTGC-TCCTTTGC
1 TTTGCTTCCTTTGC
30240045 T
1 T
30240046 AATGGCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.00, C:0.31, G:0.14, T:0.55
Consensus pattern (14 bp):
TTTGCTTCCTTTGC
Found at i:30253595 original size:38 final size:39
Alignment explanation
Indices: 30253504--30253598 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 39
30253494 CAGTACCAAT
* *
30253504 TGGTGTGTAGGGCTGGATGGGTCGATTTTATCCCCATACT
1 TGGTGTGTAGGGTTGGATGGGTCGATTTTATCCCCA-ACA
*
30253544 TGGTGTGTAGGGTTGGGTGGGTCGATTTTATCCCC-ACA
1 TGGTGTGTAGGGTTGGATGGGTCGATTTTATCCCCAACA
*
30253582 TGGTGTGTTGGGTTGGA
1 TGGTGTGTAGGGTTGGA
30253599 CGGAGATGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
38 17 0.34
40 33 0.66
ACGTcount: A:0.13, C:0.14, G:0.38, T:0.36
Consensus pattern (39 bp):
TGGTGTGTAGGGTTGGATGGGTCGATTTTATCCCCAACA
Found at i:30256537 original size:29 final size:29
Alignment explanation
Indices: 30256505--30256560 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
30256495 GCAACCTTAG
* *
30256505 GCATTTTGATCTCAATATTGCGGCATTGA
1 GCATTCTGATCCCAATATTGCGGCATTGA
* *
30256534 GCATTCTGATCCCAATGTTGTGGCATT
1 GCATTCTGATCCCAATATTGCGGCATT
30256561 CACTTGTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (29 bp):
GCATTCTGATCCCAATATTGCGGCATTGA
Found at i:30261262 original size:29 final size:29
Alignment explanation
Indices: 30261190--30261262 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
30261180 AATCTGTCAG
* * * * *
30261190 CAATGTTGCAACCTTGGGCATTTTGATCT
1 CAATGTTGCGACATTGAGCATTCTGATCC
*
30261219 CAATGTTGCGGCATTGAGCATTCTGATCC
1 CAATGTTGCGACATTGAGCATTCTGATCC
*
30261248 CAATGTTGTGACATT
1 CAATGTTGCGACATT
30261263 CACTTGCCAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (29 bp):
CAATGTTGCGACATTGAGCATTCTGATCC
Found at i:30264103 original size:19 final size:21
Alignment explanation
Indices: 30264065--30264103 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
30264055 TTAATTTTTA
*
30264065 TTTAAAATATTTAATGAATTT
1 TTTAAAATATTTAATAAATTT
30264086 TTTAAAA-A-TTAATAAATT
1 TTTAAAATATTTAATAAATT
30264104 GAAAAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TTTAAAATATTTAATAAATTT
Found at i:30264190 original size:16 final size:16
Alignment explanation
Indices: 30264171--30264217 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
30264161 ATGTTAATGT
*
30264171 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
30264187 TATTTAATATTAAAAA
1 TATTTAATATTAAAAA
30264203 TATTTAATATTAAAA
1 TATTTAATATTAAAA
30264218 TAGTATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:30264755 original size:2 final size:2
Alignment explanation
Indices: 30264748--30264879 Score: 264
Period size: 2 Copynumber: 66.0 Consensus size: 2
30264738 ATATTGCTAT
30264748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30264790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30264832 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30264874 TA TA TA
1 TA TA TA
30264880 ATAGAAATAT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 130 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30266905 original size:20 final size:20
Alignment explanation
Indices: 30266869--30266906 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30266859 AAGTGCAGTT
*
30266869 AGAGGCACAAATGTGCAATC
1 AGAGGCACAAATATGCAATC
30266889 AGAGGCACCAAA-ATGCAA
1 AGAGGCA-CAAATATGCAA
30266907 ACCCATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.11
Consensus pattern (20 bp):
AGAGGCACAAATATGCAATC
Found at i:30272179 original size:28 final size:28
Alignment explanation
Indices: 30272139--30272217 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
30272129 GCAATCAAAT
* *
30272139 ATGGCACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
30272167 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
30272195 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
30272218 CAAATGATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:30274052 original size:27 final size:27
Alignment explanation
Indices: 30273968--30274144 Score: 133
Period size: 27 Copynumber: 6.5 Consensus size: 27
30273958 AAATTGTACA
* * *
30273968 GCACTAAGTGTGCG-ATTCTACTTTGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
30273995 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
30274022 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* ** *
30274049 GCACTGAGTGTGCGGGTTTGACTATGTA
1 GCACTAAGTGTGC-GAATTGACTATGTG
* * *
30274077 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * * * *
30274104 GCACTAAATGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAATTGACTATGTG
*
30274131 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
30274145 GGCTCAATAT
Statistics
Matches: 120, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
27 96 0.80
28 24 0.20
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:30274107 original size:55 final size:54
Alignment explanation
Indices: 30273995--30274144 Score: 140
Period size: 55 Copynumber: 2.8 Consensus size: 54
30273985 CTACTTTGTT
* ** * *
30273995 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * * ** *
30274049 GCACTGAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
30274104 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
30274145 GGCTCAATAT
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
54 36 0.47
55 41 0.53
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:30274108 original size:82 final size:82
Alignment explanation
Indices: 30273964--30274146 Score: 192
Period size: 82 Copynumber: 2.2 Consensus size: 82
30273954 GATTAAATTG
* * * * *
30273964 TACAGCACTAAGTGTGC-GATTCT-ACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACT
1 TACAGCACTGAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACT
*
30274027 AAGTGTGCGAATTGACCA
65 AAATGTGCGAATTGACCA
* * ** *
30274045 TGCGGCACTGAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTGAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
30274109 AAATGTGCGAGTTGATTA
65 AAATGTGCGAATTGACCA
*
30274127 TATAGCACTGAGTGTGCGGG
1 TACAGCACTGAGTGTGCGGG
30274147 CTCAATATAC
Statistics
Matches: 82, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
81 16 0.20
82 66 0.80
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (82 bp):
TACAGCACTGAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTA
AATGTGCGAATTGACCA
Found at i:30282097 original size:55 final size:54
Alignment explanation
Indices: 30282002--30282151 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
30281992 CTACTTTGTT
* ** * *
30282002 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
30282056 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
30282111 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
30282152 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:30282114 original size:27 final size:27
Alignment explanation
Indices: 30281974--30282151 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
30281964 TAAATTGTAC
30281974 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
30282001 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
30282027 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
30282055 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
30282083 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
30282110 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
30282137 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
30282152 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:30282115 original size:82 final size:81
Alignment explanation
Indices: 30281975--30282130 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
30281965 AAATTGTACA
* * * *
30281975 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
30282040 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
30282056 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
30282119 TGTGCGAGTTGA
63 TGTGCGAATTGA
30282131 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:30284508 original size:43 final size:43
Alignment explanation
Indices: 30284447--30284597 Score: 157
Period size: 43 Copynumber: 3.5 Consensus size: 43
30284437 CCTAGACGTA
*
30284447 GTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACATG
1 GTCTTACATGAAATCAAATATCGATGCCACTGTCCCAGACATG
* * *
30284490 GTCTTACAAGAAAACAAATAT-GATGTCGA-TGTCCCAGACATG
1 GTCTTACATGAAATCAAATATCGATG-CCACTGTCCCAGACATG
* * *
30284532 GTTTTACATGTAAATCTCAA-ATCGATGCCAAC-ATCCCAGACATG
1 GTCTTACATG-AAATC-AAATATCGATGCC-ACTGTCCCAGACATG
* *
30284576 GTCTTACACGAAATCACATATC
1 GTCTTACATGAAATCAAATATC
30284598 AGAATCCTAT
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
42 26 0.30
43 35 0.40
44 26 0.30
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (43 bp):
GTCTTACATGAAATCAAATATCGATGCCACTGTCCCAGACATG
Found at i:30284981 original size:16 final size:16
Alignment explanation
Indices: 30284960--30284991 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30284950 ATTAGCCCTC
*
30284960 ATATTTTCACATTTTA
1 ATATTTTAACATTTTA
30284976 ATATTTTAACATTTTA
1 ATATTTTAACATTTTA
30284992 GTCCTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTTAACATTTTA
Found at i:30285885 original size:24 final size:26
Alignment explanation
Indices: 30285842--30285889 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
30285832 ATGCCAAAAC
*
30285842 ATTTATGTGTTTAGGTTGATTTTAAA
1 ATTTATGTGTTGAGGTTGATTTTAAA
30285868 ATTTATGT-TTGAGG-TGATTTTA
1 ATTTATGTGTTGAGGTTGATTTTA
30285890 GGCATATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 5 0.24
26 8 0.38
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (26 bp):
ATTTATGTGTTGAGGTTGATTTTAAA
Found at i:30291026 original size:14 final size:15
Alignment explanation
Indices: 30291009--30291037 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30290999 TCACGGAAAT
30291009 TTCACACAT-ATAAA
1 TTCACACATAATAAA
30291023 TTCACACATAATAAA
1 TTCACACATAATAAA
30291038 CATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:30299727 original size:54 final size:55
Alignment explanation
Indices: 30299599--30299728 Score: 145
Period size: 56 Copynumber: 2.4 Consensus size: 55
30299589 TTTGATGACA
* * *
30299599 TGATACATGCTAGGTTCGGGAGCTTGTGTAGCCCTATTGAAAGGCATGTAATTATG
1 TGATACATGCTAGGTCCGGGAGCTTATGTAGCCCTATTGAAAGG-ATGTAATAATG
* * * * * **
30299655 TGGTACACGCTAGGTCCGGGAGCTTATGTAGCCTTGTTGAGAGG-TGTGGTAATG
1 TGATACATGCTAGGTCCGGGAGCTTATGTAGCCCTATTGAAAGGATGTAATAATG
*
30299709 TGATGCATGCTAGGTCCGGG
1 TGATACATGCTAGGTCCGGG
30299729 TACTCATGAT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 24 0.39
56 37 0.61
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (55 bp):
TGATACATGCTAGGTCCGGGAGCTTATGTAGCCCTATTGAAAGGATGTAATAATG
Found at i:30307188 original size:56 final size:54
Alignment explanation
Indices: 30307093--30307249 Score: 163
Period size: 56 Copynumber: 2.8 Consensus size: 54
30307083 TTTGATGACA
* * * *
30307093 TGATACATGCTAGGTCCGAGAGCTTGTGTAGCCCCGTTGAGAGGCAT-GTAATTATG
1 TGATACATGCTAGGTCTGGGAGCTTATGTAGCCCTGTTGAGAGGCATGGT-A--ATG
* * * *
30307149 TGGTACACGCTAGGTCTGGGAGCTTATGTAGCCTTGTTGAGAGGCGTGGTAATG
1 TGATACATGCTAGGTCTGGGAGCTTATGTAGCCCTGTTGAGAGGCATGGTAATG
* * *
30307203 TGATGCATGCTAGGTCTGGGTGCTCATATGTAGCCCTATTGAGAGGC
1 TGATACATGCTAGGTCTGGGAGCT--TATGTAGCCCTGTTGAGAGGC
30307250 GTGCTATGTC
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
54 23 0.27
56 59 0.70
57 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (54 bp):
TGATACATGCTAGGTCTGGGAGCTTATGTAGCCCTGTTGAGAGGCATGGTAATG
Found at i:30313477 original size:26 final size:27
Alignment explanation
Indices: 30313447--30313503 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
30313437 GGTCATTAAG
*
30313447 ACCCTGGT-TTGTAAAATCACCGAAAT
1 ACCCTGGTAGTGTAAAATCACCGAAAT
* * *
30313473 ACCCTTGTAGTGTAAAATGACCGTAAT
1 ACCCTGGTAGTGTAAAATCACCGAAAT
30313500 ACCC
1 ACCC
30313504 CTGTATGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (27 bp):
ACCCTGGTAGTGTAAAATCACCGAAAT
Found at i:30313520 original size:27 final size:27
Alignment explanation
Indices: 30313456--30313508 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
30313446 GACCCTGGTT
* *
30313456 TGTAAAATCACCGAAATACCCTTGTAG
1 TGTAAAATGACCGAAATACCCCTGTAG
*
30313483 TGTAAAATGACCGTAATACCCCTGTA
1 TGTAAAATGACCGAAATACCCCTGTA
30313509 TGGTAGAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (27 bp):
TGTAAAATGACCGAAATACCCCTGTAG
Found at i:30313792 original size:22 final size:22
Alignment explanation
Indices: 30313754--30313796 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30313744 CTACGATATT
30313754 TACGGTCTTTAGCCGTTCTGTC
1 TACGGTCTTTAGCCGTTCTGTC
*
30313776 TACGGT-TTTGAGTCGTTCTGT
1 TACGGTCTTT-AGCCGTTCTGT
30313797 TGACTTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.44
Consensus pattern (22 bp):
TACGGTCTTTAGCCGTTCTGTC
Found at i:30313967 original size:27 final size:28
Alignment explanation
Indices: 30313937--30313996 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
30313927 GCATCTGATA
*
30313937 CTGATTCTG-TGTTGGGCTT-AGGCCCAC
1 CTGATTCTGTTATTGGG-TTAAGGCCCAC
30313964 CTGATTCTGTTATTGGGTTAAGGCCCAC
1 CTGATTCTGTTATTGGGTTAAGGCCCAC
30313992 CTGAT
1 CTGAT
30313997 ACTATTTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (28 bp):
CTGATTCTGTTATTGGGTTAAGGCCCAC
Found at i:30319045 original size:50 final size:46
Alignment explanation
Indices: 30318974--30319089 Score: 133
Period size: 46 Copynumber: 2.4 Consensus size: 46
30318964 TGTCTTCGAC
** * *
30318974 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCC----ATATATCTAAT
* * *
30319024 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATCTAAT
30319070 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
30319090 TCTGTCCTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 29 0.50
50 29 0.50
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCATATATCTAAT
Found at i:30320400 original size:6 final size:6
Alignment explanation
Indices: 30320365--30320477 Score: 54
Period size: 6 Copynumber: 18.5 Consensus size: 6
30320355 AAGAAACATT
* * * *
30320365 ATCAGA A-CTAGA ATCAAA ATGAGG ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * * * *
30320414 ATCAGA ATTAGA ATTAG- GTGACAGA ATCAGA ATTAGT AT-AGA TAACAGA
1 ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA -ATCAGA
30320463 ATCAGA ATCAGA ATC
1 ATCAGA ATCAGA ATC
30320478 TAAATGCAAT
Statistics
Matches: 80, Mismatches: 17, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
5 5 0.06
6 64 0.80
7 9 0.11
8 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:30320420 original size:25 final size:25
Alignment explanation
Indices: 30320389--30320477 Score: 117
Period size: 25 Copynumber: 3.6 Consensus size: 25
30320379 CAAAATGAGG
30320389 ATCAGAATCAGAATCAGGTGACAGA
1 ATCAGAATCAGAATCAGGTGACAGA
* *
30320414 ATCAGAATTAGAATTAGGTGACAGA
1 ATCAGAATCAGAATCAGGTGACAGA
* * * *
30320439 ATCAGAATTAGTAT-AGATAACAGA
1 ATCAGAATCAGAATCAGGTGACAGA
30320463 ATCAGAATCAGAATC
1 ATCAGAATCAGAATC
30320478 TAAATGCAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
24 20 0.36
25 36 0.64
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (25 bp):
ATCAGAATCAGAATCAGGTGACAGA
Found at i:30320657 original size:27 final size:27
Alignment explanation
Indices: 30320594--30320674 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
30320584 AGCATGGTTG
* * *
30320594 CCAGA-ACAGATATTGTGACAGAGTCA
1 CCAGATACAAATATTGTGGCAGAGCCA
*
30320620 CCATATACAAATATTGTGGCAGAGCCA
1 CCAGATACAAATATTGTGGCAGAGCCA
* * *
30320647 CCAGAGT-CAAATAATGTGGTAAAGCCA
1 CCAGA-TACAAATATTGTGGCAGAGCCA
30320674 C
1 C
30320675 TTAACAGAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
26 4 0.09
27 40 0.89
28 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (27 bp):
CCAGATACAAATATTGTGGCAGAGCCA
Found at i:30320770 original size:22 final size:22
Alignment explanation
Indices: 30320745--30320805 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
30320735 AATAATGACA
*
30320745 CACACAGCCATAATCAGGTTGG
1 CACAAAGCCATAATCAGGTTGG
30320767 CACAAAGCCATATAT-AGGTTGG
1 CACAAAGCCATA-ATCAGGTTGG
*
30320789 CGCAAAGCCATAATCAG
1 CACAAAGCCATAATCAG
30320806 AATAATTGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (22 bp):
CACAAAGCCATAATCAGGTTGG
Found at i:30322796 original size:47 final size:47
Alignment explanation
Indices: 30322743--30323278 Score: 957
Period size: 47 Copynumber: 11.4 Consensus size: 47
30322733 CCTTCACATC
30322743 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
30322790 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
30322837 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
30322884 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
30322931 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
*
30322978 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATTGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
* * * * *
30323025 TTCGGACTTATCACATATATACACTTTCAAATTCATCACATTGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
*
30323072 TTAGG-CTTTATCACATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGTC-TTATCTCATATATACACTTTCACATTCATCACATCGGCCA
30323119 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
30323166 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
*
30323213 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATTGGCCA
1 TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
* * *
30323260 TTCGGCCTTATCACATATA
1 TTAGGTCTTATCTCATATA
30323279 CATATCTTGT
Statistics
Matches: 474, Mismatches: 13, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
46 1 0.00
47 472 1.00
48 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (47 bp):
TTAGGTCTTATCTCATATATACACTTTCACATTCATCACATCGGCCA
Found at i:30322807 original size:80 final size:80
Alignment explanation
Indices: 30322669--30322821 Score: 234
Period size: 80 Copynumber: 1.9 Consensus size: 80
30322659 CCCTTCGGGA
* * *
30322669 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
30322734 CTTCACATCTTAGGT
66 CTTCACATCTTAGGT
* * * *
30322749 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGTCTTATCTCATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
30322814 TTTCACAT
66 CTTCACAT
30322822 TCATCACATC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.28, C:0.29, G:0.07, T:0.37
Consensus pattern (80 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
CTTCACATCTTAGGT
Found at i:30325759 original size:27 final size:27
Alignment explanation
Indices: 30325729--30325844 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
30325719 GGATGTCACA
* *
30325729 GGTATCTCGGTAATTCTACGCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAAG
* *
30325756 GGTATTTCTGTATTTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAAG
*
30325783 GGTATTTTGGTAATTCTACCCTAC-AG
1 GGTATTTCGGTAATTCTACCCTACAAG
* *
30325809 GAGTATTTCAGTAATTCTACCCTACAGG
1 G-GTATTTCGGTAATTCTACCCTACAAG
30325837 GGTATTTC
1 GGTATTTC
30325845 AATAATTTTG
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.04
27 72 0.94
28 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTACAAG
Found at i:30325920 original size:27 final size:27
Alignment explanation
Indices: 30325872--30325923 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
30325862 AGGGTAAAAC
** *
30325872 GGTAATTTTGTAAATCGGGGGTATTTT
1 GGTAATTTTACAAATCGAGGGTATTTT
*
30325899 GGTAATTTTACAAGTCGAGGGTATT
1 GGTAATTTTACAAATCGAGGGTATT
30325924 CCAGTAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.29, T:0.40
Consensus pattern (27 bp):
GGTAATTTTACAAATCGAGGGTATTTT
Found at i:30329421 original size:14 final size:15
Alignment explanation
Indices: 30329392--30329421 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30329382 TGTGAAGAAA
30329392 TATTTTTCTTCTCCT
1 TATTTTTCTTCTCCT
30329407 TATTTTTCTTC-CCT
1 TATTTTTCTTCTCCT
30329421 T
1 T
30329422 GGTCGAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTCTTCTCCT
Found at i:30335360 original size:19 final size:20
Alignment explanation
Indices: 30335318--30335361 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
30335308 GAAAAAAAAT
30335318 CAAAAGTAAGAACGACAAGA
1 CAAAAGTAAGAACGACAAGA
30335338 -AAAAGTACAGAAC-A-AAGA
1 CAAAAGTA-AGAACGACAAGA
30335356 CAAAAG
1 CAAAAG
30335362 CATTGTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.18
19 13 0.59
20 5 0.23
ACGTcount: A:0.64, C:0.14, G:0.18, T:0.05
Consensus pattern (20 bp):
CAAAAGTAAGAACGACAAGA
Found at i:30338933 original size:13 final size:13
Alignment explanation
Indices: 30338915--30338944 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30338905 TTAGTATAGT
30338915 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
30338928 AAAAAGAAAGAAG
1 AAAAAGAAAAAAG
30338941 AAAA
1 AAAA
30338945 GAAGAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:30338946 original size:18 final size:17
Alignment explanation
Indices: 30338917--30338953 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
30338907 AGTATAGTAA
30338917 AAAGAAAAAAGAAAAAG
1 AAAGAAAAAAGAAAAAG
*
30338934 AAAGAAGAAAAGAAGAAG
1 AAAGAA-AAAAGAAAAAG
30338952 AA
1 AA
30338954 TGCACAGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAAG
Found at i:30342979 original size:6 final size:6
Alignment explanation
Indices: 30342968--30343001 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
30342958 CGGAATATAA
* *
30342968 AGAGGG AGAGGG AGAGGG AGAGAG AGAGAG AGAG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAG
30343002 AAGAATAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:30350498 original size:5 final size:5
Alignment explanation
Indices: 30350488--30350516 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
30350478 AAAAGGTAAA
30350488 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
30350517 AAGAACCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:30353908 original size:88 final size:88
Alignment explanation
Indices: 30353813--30353974 Score: 315
Period size: 88 Copynumber: 1.8 Consensus size: 88
30353803 TCATATTTTG
30353813 TTTTATATTATTTTTTAAAATTTATAAATAAATTATGGTTTTCTATAAATTCTTTATAAAATTTA
1 TTTTATATTATTTTTTAAAATTTATAAATAAATTATGGTTTTCTATAAATTCTTTATAAAATTTA
30353878 TACATTTTTTTAACCACATCATA
66 TACATTTTTTTAACCACATCATA
*
30353901 TTTTATATTATTTTTTAAATTTTATAAATAAATTATGGTTTTCTATAAATTCTTTATAAAATTTA
1 TTTTATATTATTTTTTAAAATTTATAAATAAATTATGGTTTTCTATAAATTCTTTATAAAATTTA
30353966 TACATTTTT
66 TACATTTTT
30353975 AACCATGTAC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (88 bp):
TTTTATATTATTTTTTAAAATTTATAAATAAATTATGGTTTTCTATAAATTCTTTATAAAATTTA
TACATTTTTTTAACCACATCATA
Found at i:30356107 original size:42 final size:43
Alignment explanation
Indices: 30356061--30356176 Score: 162
Period size: 43 Copynumber: 2.7 Consensus size: 43
30356051 ATATGTGTTA
30356061 TCGTGTAAGACCATGTCTGGGACATTGGCAT-CATATTTGATT
1 TCGTGTAAGACCATGTCTGGGACATTGGCATCCATATTTGATT
* * *
30356103 TCGTGTAAGACCCTGTCTGGGACAGTGGTATCCATATTTGATT
1 TCGTGTAAGACCATGTCTGGGACATTGGCATCCATATTTGATT
* * * *
30356146 ACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TCGTGTAAGACCATGTCTGGGACATTGGCAT
30356177 TGATGAGCTT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 28 0.44
43 35 0.56
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGACATTGGCATCCATATTTGATT
Found at i:30358783 original size:47 final size:48
Alignment explanation
Indices: 30358619--30358793 Score: 149
Period size: 47 Copynumber: 3.6 Consensus size: 48
30358609 GATGTGTCAA
* * * * * *
30358619 TGTAAGACCATGTCTGGGAAATGGCATTGGCACAAATATATGA-GAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTC-AAT-T-CGATGAGCCAG
** * *
30358669 TGTAAGACCATGTCTGGGACATGGGGTCGGCCTCAATTTCGAT-AGTCAG
1 TGTAAGACCATGTCTGGGACATGGCATC-GACTCAA-TTCGATGAGCCAG
* * ** *
30358718 TGTAAGACTATGTTTGGGACATGGCATCGACTTGA-TGGATGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTCAATTCGATGAGCCAG
30358765 TGTAAGACCATGTCTGGGACATGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATCG
30358794 GCATTATACC
Statistics
Matches: 101, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
46 4 0.04
47 32 0.32
48 4 0.04
49 30 0.30
50 27 0.27
51 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGACTCAATTCGATGAGCCAG
Found at i:30364126 original size:25 final size:25
Alignment explanation
Indices: 30364098--30364147 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
30364088 TTTCTAGTCA
30364098 GGGATACAGAGTTTTTGAAAGTATC
1 GGGATACAGAGTTTTTGAAAGTATC
30364123 GGGATACAGAGTTTTTGAAAGTATC
1 GGGATACAGAGTTTTTGAAAGTATC
30364148 CCTGTGGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (25 bp):
GGGATACAGAGTTTTTGAAAGTATC
Found at i:30365813 original size:47 final size:44
Alignment explanation
Indices: 30365755--30365872 Score: 130
Period size: 47 Copynumber: 2.5 Consensus size: 44
30365745 GTGCTAGTGT
*
30365755 AAGACATGTCTGGGACATGCATCAGCCACATT-ATGAGAGCCACTGC
1 AAGACATGTCTGGGACATGCATC-G--ACATTAACGAGAGCCACTGC
* * *
30365801 AAGACCATGTCTGGGACATGGCATCGACATTGAAACGAGAGCTAGTGT
1 AAGA-CATGTCTGGGACAT-GCATCGACATT--AACGAGAGCCACTGC
30365849 AAGACATGTCTGGGACATGCATCG
1 AAGACATGTCTGGGACATGCATCG
30365873 GCTACGAGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
45 5 0.08
46 10 0.16
47 29 0.46
48 19 0.30
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (44 bp):
AAGACATGTCTGGGACATGCATCGACATTAACGAGAGCCACTGC
Found at i:30380643 original size:42 final size:41
Alignment explanation
Indices: 30380584--30380705 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 41
30380574 TAGGGTTATT
30380584 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TGAGATT-CGTGTAAGACCATATCTGGGATATGGCATCGATA
* *
30380626 TGAGACTTCGTGTAAGACCATAGCT-AGACTATTGGCATCGATA
1 TGAGA-TTCGTGTAAGACCATATCTGGGA-TA-TGGCATCGATA
* *
30380669 TGAGATCCCATGTAAGACCATATCTGGGATATGGCAT
1 TGAGAT-TCGTGTAAGACCATATCTGGGATATGGCAT
30380706 TGGCATGGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
41 2 0.03
42 30 0.43
43 35 0.51
44 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (41 bp):
TGAGATTCGTGTAAGACCATATCTGGGATATGGCATCGATA
Done.